Figure 2: Characterization of stationary phase mitophagy in WT and KO strains by quantitative proteomics. | Nature Communications

Figure 2: Characterization of stationary phase mitophagy in WT and KO strains by quantitative proteomics.

From: Involvement of mitochondrial dynamics in the segregation of mitochondrial matrix proteins during stationary phase mitophagy

Figure 2

(a) Global protein abundance dynamics was analysed in four different of S. cerevisiae strains (WT, pep4Δ, atg32Δ and aup1Δ) using SILAC. Global protein levels were analysed over 5-day incubations in lactate-based minimal medium. (b) To quantify changes in protein dynamics, each of the strains was labelled in lactate-based minimal media containing either normal lysine (Lys0), lysine-D4 (Lys4) or lysine-13C6 15N2 (Lys8). Samples (10 OD600 units) were taken at day 1 (Lys0), day 2 (Lys4), day 3 (Lys8), day 4 (Lys4) and day 5 (Lys8; see Methods). The mixed lysates were then separated by one-dimensional SDS–polyacrylamide gel electrophoresis and the proteins were digested with LysC. The resulting peptides were analysed by liquid chromatography-tandem mass spectrometry and the raw data were processed by MaxQuant. We performed two biological replicates of the complete time course experiments for each mutant, and three replicates for the WT, and observed good reproducibility for all the individual experiments (Supplementary Fig. S2). (c) Density plot of the reproducibility of biological replicates. (d) Venn diagram of the number of proteins identified from the different yeast strains. (e) Principal component analysis of the log2-transformed abundance changes of proteins were identified in all strains and all time points.

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